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Berger & Munson (1991) CABIOS 7:479 -based on
Murata below but with random, iterative search instead of exhaustive: MUSEQAL.
Bron & Kerbrosch (1973) Commun. Assoc. Computing Machinery 16:311 - an earlier compatability algorithm. Cabot & Beckenbach (1989) CABIOS 5:233 - the eyeball sequence editor leaves judgment of alignments to you: ESEE. Cavalli-Sforza & Edwards (1967) Evolution 32:550 - an early development of the distance method for making trees. Cavendar & Felsenstein (1987) J. Classif. 4:57 - evolutionary invariants. Clayton & Gee 1993 Nature 365:111 - review of MHC selection. Corpet (1988) Nuc. Acids. Res. 16:10881 -algorithm similar to CLUSTAL but nice interface: MULTALIN. Eanes et al. 1993 PNAS 90:7475 - test of selection vs nonadaptive evolution. Estabroook et al (1976) Math. Biosci. 23:187 - the compatability algorithm (one version) Farris (1970) Syst. Zool. 19:83 - early UPGMA. Felsenstein (1978) Syst. Zool. 27:401- demonstration that parsimony fails if rates on branches differ greatly Felsenstein (1981) J. Mol. Evol. 17:368 - introduction of the maximum likelihood algorithm. Felsenstein (1985) Evol. 39:783 - bootstrapping applied to ML trees. Fitch & Margoliash (1967) Science 155:279 - another ealy development of the distance method for making trees. Fitch & Markowitz (1970) Biochem. Genet. 4:579 - covarion concept. Fitch (1971) Syst. Zool. 20:406 - exposition of the distance method for making trees. Fitch & Smith (1983) Proc. Nat. Acad. Sci. USA 80:1382 - tested various gap penalties and showed results depend on penalty. Gibbs & McIntyre (1970) Eur. J. Biochem. 16:1- original dot matrix algorithm Gotoh (1982) J. Mol. Biol. 162:705 - modified N-W algorithm that searches diagonally rather than along matrix axes. Gotoh (1986) J. Theoret. Biol. 121:327 - improvements for multiple sequence alignment. Hendy & Penny (1982) Math. Biosci. 59:277 used a branch and bound algorithm to find all most parsimonious trees Hendy & Penny (1989) Syst. Zool. 38:297 - another modeling challenge to parsimony Henikoff (1993) TIBS 18:267 - how to email searches. Higgins (1992) CABIOS 8:189 - improved the heuristic algorithm that I think could be given a theoretical basis: CLUSTALV. Higgins & Sharp (1988) Gene 73:237 and (1989) CABIOS 5:151 - developed an heuristic algorithm: CLUSTAL. Hudson 1993 PNAS 90:7425 - commentary on #Eanes (1993) above. Jukes & Kantor (1969) in Mammalian Protein Metabolism (ed by H.N. Munro) Academic Press (NY) p21 - model for substitution rates. Karlin et al (1983) Proc. Nat. Acad. Sci. USA 80:5660 - improvements for multiple sequence alignment.Karlin et al (1992) Mol. Biol. Evol. 9:152 - developing criteria to distinguish conserved vs nonconserved sites for stabilizing vs modifying selection. Keim et al (1981) J. Mol. Biol. 151:179 - the only reference I have so far for Fitch's test for divergence vs. convergence. Kimura (1968) Nature 217:624 - statement of the neutral theory of evolutionary change. Kimura (1980) J. Mol. Evol. 16:111 - 2 parameter model for rates in ML. Kimura & Ohta (1971) Nature 229:467 - neutral theory applied to polymorphisms. Kishino & Hasegawa (1989) J. Mol. Evol. 29:170 - Paired sites test based on ML extended. (1969) Syst. Zool. 18:1 - early UPGMA.Lake (1987) Mol. Biol. Evol. 4:167 {nearly impenetrable} - evolutionary parsimony. Le Quesne (1969) Syst. Zool. 18:1 - the compatability concept.Lipman & Pearson (1985) Science 227:1435 FASTP makes k-tuple look up tables. Maizel & Lenk (1981) Proc. Nat. Acad. Sci. USA 78:7665 - Improved dot matrix algorithm for DNA & RNA. Mazodier & Davis (1991) Ann. Rev. Genet. 25:147 - DNA exchange across conventional species and genus lines in bacteria. Murata et al (1985) Proc. Nat. Acad. Sci. USA 82:3073 - improvements for multiple sequence alignment. Navidi et al (1991) Mol. Biol. Evol. 8:128 - Moving evolutionary parsimony / invariants to >4 has proved intractable so far; but have begun to solve 5. Navidi et al (1993) Biometrics 49:543 - more on solving larger invariants. Needleman & Wunsch (1970) J. Mol. Biol. 48:443 - a dynamic programming algorithm for aligning two sequences. Pustell & Kafatos (1982) Nuc. Acids Res. 10:4765 modified dot matrix algorithm to dampen short diagonals and show stringencies via letters (A best, B next, etc) or colors Saitou & Nei (1987) Mol. Biol. Evol. 4:406 - the neighbor joining algorithm for making trees from distance data Sellers (1974) SIAM J. Appl. Math. 26:787 - a distinct (from N-W above) but related alignment algorithm. Shoemaker & Fitch (1989) Mol. Biol. Evol. 6:270 - covariotides, an extension of covarions. Staden (1982) Nuc. Acids Res. 10:2951 also fixed protein version of dot matrix algorithm to allow for similarities (mutation matrix introduced by Dayhoff) among amino acids. Stewart & Wilson (1987) Cold Spring Harbor Sympos. Quant. Biol. 52:891- similarities in lysozyme in langurs vs. cows may be due to convergence. Stolzfuss & Milkman (1988) Genetics 120:359 -f genetic variation in DNA of populations of E. coli indicates that clonal segments of DNA appear to be replaced not individual bases. Strimmer & von Haeseler (1997) Proc. Nat. Acad. Sci. USA 94:6815 - Puzzle a likelihood-mapping method to visualize phylogenetic content of a sequence alignment. Studier & Keppler (1988) Mol. Biol. Evol. 5:729 - modified the neighbor joining algorithm to make it more efficient. Templeton (1983) Evol. 37:221 - applied paired sites test to parsimony by using # steps Thorne et al (1992) J. Mol. Evol. 34:3 beginning to solve ML alignment problem. Wagner and Camin & Sokal (1965) Evol. 19:311 - parsimony as introduced for systematics (I have a suspicion there are actually two refs here -- if anyone separates them, let me know) White et al (1984) Nuc. Acids Res. 12:751 modified dot matrix algorithms to search along diagonal (more efficient) Wheelis et al (1992) Proc. Natl. Acad. Sci. USA 89:2930 - a microbiologically inspired analysis of cladistics via phylogenetics .Wilbur & Lipman (1983) Proc. Nat. Acad. Sci. USA 80:726 FASTA makes k-tuple look up tables. |
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